Ricardo Wurmus
f21c711a0f
gnu: kallisto: Update to 0.46.2.
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* gnu/packages/bioinformatics.scm (kallisto): Update to 0.46.2.
[source]: Remove bundled htslib sources.
2021-03-02 17:06:58 +01:00
Ricardo Wurmus
cc39e9dbdc
gnu: kallisto: Use older htslib.
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* gnu/packages/bioinformatics.scm (kallisto)[inputs]: Use htslib-1.9 instead
of the latest.
2021-03-02 17:06:58 +01:00
Nicolas Goaziou
3759df574d
gnu: f-seq: Use HTTPS home page URI.
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* gnu/packages/bioinformatics.scm (f-seq)[home-page]: Use HTTPS URI.
2021-02-28 11:03:56 +01:00
Ricardo Wurmus
5d5bbd6fcc
gnu: Add star-for-pigx.
...
This is a follow-up to commit f1f6e49190
2021-02-23 19:40:59 +01:00
Ricardo Wurmus
f1f6e49190
gnu: star: Update to 2.7.8a.
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* gnu/packages/bioinformatics.scm (star): Update to 2.7.8a.
2021-02-22 21:16:19 +01:00
Ricardo Wurmus
f310b06685
gnu: nanopolish: Fix script wrapping.
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* gnu/packages/bioinformatics.scm (nanopolish)[arguments]: Fix wrap-programs
phase.
[inputs]: Add Guile for wrap-script; add bioperl and perl-getopt-long for Perl
scripts.
2021-02-19 23:35:04 +01:00
Ricardo Wurmus
15c0cc4aa2
gnu: Add prinseq.
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* gnu/packages/bioinformatics.scm (prinseq): New variable.
2021-02-19 23:14:59 +01:00
Ricardo Wurmus
80d3150c94
gnu: Add ngshmmalign.
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* gnu/packages/bioinformatics.scm (ngshmmalign): New variable.
2021-02-19 17:24:52 +01:00
Ricardo Wurmus
8360705948
gnu: Add r-archr.
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* gnu/packages/bioinformatics.scm (r-archr): New variable.
2021-02-18 16:11:38 +01:00
Ricardo Wurmus
9904a15a4c
gnu: Add indelfixer.
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* gnu/packages/bioinformatics.scm (indelfixer): New variable.
2021-02-15 13:51:58 +01:00
Mădălin Ionel Patrașcu
160e4a95e7
gnu: bowtie1: Update to 1.3.0.
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* gnu/packages/bioinformatics.scm (bowtie1): Update to 1.3.0.
[arguments]: Set CC in make flags.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2021-02-11 22:29:37 +01:00
Ricardo Wurmus
0e3e26ca60
gnu: r-gage: Update to 2.40.1.
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* gnu/packages/bioinformatics.scm (r-gage): Update to 2.40.1.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
5103da059a
gnu: r-msnbase: Update to 2.16.1.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.16.1.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
2596200514
gnu: r-methylkit: Update to 1.16.1.
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* gnu/packages/bioinformatics.scm (r-methylkit): Update to 1.16.1.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
3f7e96acc7
gnu: r-delayedarray: Update to 0.16.1.
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* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.16.1.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
9b66b8017d
gnu: r-biomart: Update to 2.46.3.
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* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.46.3.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
8e25b1acf9
gnu: r-edger: Update to 3.32.1.
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* gnu/packages/bioinformatics.scm (r-edger): Update to 3.32.1.
2021-02-11 21:33:38 +01:00
Ricardo Wurmus
809f725977
gnu: r-iranges: Update to 2.24.1.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.24.1.
2021-02-11 21:33:37 +01:00
Ricardo Wurmus
88fd569ddf
gnu: r-s4vectors: Update to 0.28.1.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.28.1.
2021-02-11 21:33:37 +01:00
Ricardo Wurmus
babb2dce34
gnu: r-systempiper: Update to 1.24.3.
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* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.24.3.
2021-02-11 21:33:37 +01:00
Ricardo Wurmus
d3ac91dd9d
gnu: r-gseabase: Update to 1.52.1.
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* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.52.1.
2021-02-11 21:33:37 +01:00
Ricardo Wurmus
074d142ab6
gnu: r-genefilter: Update to 1.72.1.
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* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.72.1.
2021-02-11 21:33:37 +01:00
Ricardo Wurmus
8d61539883
gnu: rsem: Link with shared libhts library.
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* gnu/packages/bioinformatics.scm (rsem)[arguments]: Link with libhts.so
instead of libhts.a.
2021-02-05 23:30:43 +01:00
877ab0266c
gnu: vcflib: Fix generated pkg-config file.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: In custom
generated pkg-config file, link with all needed libraries and
fix linker library.
* gnu/packages/patches/freebayes-devendor-deps.patch: Adjust accordingly.
2021-02-01 19:02:14 +02:00
Maxim Cournoyer
23a5dcce1d
gnu: grocsvs: Remove package.
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This package depends on Python 2 and doesn't build anymore. Upstream doesn't
seem active, but if they ever port it to Python 3, they should let people know
here: https://github.com/grocsvs/grocsvs/issues/6 .
* gnu/packages/bioinformatics.scm (grocsvs): Delete.
2021-01-29 10:58:25 -05:00
Ricardo Wurmus
c4a2cbeb06
gnu: Add r-demultiplex.
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* gnu/packages/bioinformatics.scm (r-demultiplex): New variable.
2021-01-28 22:24:51 +01:00
Ricardo Wurmus
04b1a1f6bd
gnu: Add repeat-masker.
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* gnu/packages/bioinformatics.scm (repeat-masker): New variable.
2021-01-28 15:07:55 +01:00
Ricardo Wurmus
6d3cafa086
gnu: Add trf.
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* gnu/packages/bioinformatics.scm (trf): New variable.
2021-01-28 15:07:55 +01:00
b3e39a475f
gnu: freebayes: Update source, home-page URIs.
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* gnu/packages/bioinformatics.scm (freebayes)[source]: Update to new
upstream URI.
[home-page]: Same.
2021-01-19 11:48:38 +02:00
99043adf46
gnu: freebayes: Don't include vcflib sources.
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* gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Remove
vcflib-source, intervaltree-source. Move vcflib ...
[inputs]: ... to here.
[arguments]: Adjust 'patch-source and 'unpack-submodule-sources for
changes in vendored code.
* gnu/packages/patches/freebayes-devendor-deps.patch: Update patch.
2021-01-19 11:41:07 +02:00
1bbfe1789d
gnu: vcflib: Add pkg-config file.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
create pkg-config file.
2021-01-19 11:36:01 +02:00
d6a8148c8d
gnu: vcflib: Build a shared library.
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* gnu/packages/bioinformatics.scm (vcflib)[arguments]: Add phase to
build a shared library instead of a static one.
2021-01-19 10:43:06 +02:00
797585746b
gnu: freebayes: Extend test timeout on slower architectures.
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* gnu/packages/bioinformatics.scm (freebayes)[arguments]: Use custom
'check phase on aarch64-linux and armhf-linux to extend the test timeout.
2021-01-19 10:33:19 +02:00
Mădălin Ionel Patrașcu
c0afd8044f
gnu: Add r-snapatac.
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* gnu/packages/bioinformatics.scm (r-snapatac): New variable.
2021-01-18 23:26:53 +01:00
Mădălin Ionel Patrașcu
2d9c6542c8
gnu: mafft: Update to 7.475.
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* gnu/packages/bioinformatics.scm (mafft): Update to 7.475.
Signed-off-by: Efraim Flashner <efraim@flashner.co.il>
2021-01-18 11:57:28 +02:00
6cb86e23a9
gnu: ruby-bio-vcf: Rename to bio-vcf.
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This package is widely known in select circles specifically as 'bio-vcf'.
* gnu/packages/bioinformatics.scm (ruby-bio-vcf): Rename to bio-vcf.
2021-01-18 11:19:37 +02:00
9b6cddd32d
gnu: Add ruby-bio-vcf.
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* gnu/packages/bioinformatics.scm (ruby-bio-vcf): New variable.
2021-01-18 10:41:46 +02:00
fc9fd5496f
gnu: freebayes: Update to 1.3.3.
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* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.3.
[source]: Add patch. Add snippet to remove vendored library.
[build-system]: Switch to meson-build-system.
[inputs]: Remove bamtools. Add fastahack, smithwaterman, tabixpp.
[native-inputs]: Remove procps, python-2, tabixpp source, smithwaterman
source, multichoose source, fsom source, filevercmp source, fastahack
source, bash-tap source. Add bash-tap, grep, pkg-config, simde, vcflib.
[arguments]: Drop make-flags. Don't delete 'configure phase. Delete
custom 'fix-tests, 'build-tabixpp-and-vcflib, 'fix-makefiles, 'install
phases. Adjust 'unpack-submodule-sources phase to changed native-inputs.
Add new 'patch-source phase.
2021-01-17 15:47:32 +02:00
3ddeefe854
gnu: multichoose: Install header files.
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* gnu/packages/bioinformatics.scm (multichoose)[arguments]: Adjust
'install phase to also install header files.
2021-01-17 15:47:32 +02:00
976603b909
gnu: filevercmp: Install header files.
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* gnu/packages/bioinformatics.scm (filevercmp)[arguments]: Adjust
'install phase to install header files.
2021-01-17 15:47:32 +02:00
93309e25c7
gnu: vcflib: Update to 1.0.2.
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* gnu/packages/bioinformatics.scm (vcflib): Update to 1.0.2.
[source]: Download using git-fetch. Remove patch. Update snippet to use
packaged libraries.
[build-system]: Switch to cmake-build-system.
[inputs]: Add bzip2.
[native-inputs]: Add package-source of fsom.
[arguments]: Delete custom 'set-flags, 'install phases. Don't delete
'configure phase. Adjust 'unpack-submodule-sources phase.
* gnu/packages/patches/vcflib-use-shared-libraries.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2021-01-14 20:43:31 +02:00
db30d6eada
gnu: sambamba Update to 0.8.0.
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* gnu/packages/bioinformatics.scm (sambamba): Update to 0.8.0.
[source, home-page]: Update to new upstream URI.
[arguments]: Shorten 'fix-ldc-version phase. Remove
'place-biod-and-undead phase. Update 'unbundle-prerequisites and
'insatll phases.
[native-inputs]: Remove rdmd, biod. Move ldc ...
[inputs]: ... to here. Add zlib.
(htslib-for-sambamba): Remove variable.
2021-01-14 20:43:31 +02:00
2051be4f4c
gnu: gemma: Enable tests.
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* gnu/packages/bioinformatics.scm (gemma)[source]: Add snippet to remove
bundled sources.
[native-inputs]: Add catch-framework2-1, perl, shunit2, which.
[arguments]: Don't disable tests. Override 'check phase.
2021-01-14 20:43:31 +02:00
daf96e704d
gnu: gemma: Add Texinfo markup.
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* gnu/packages/bioinformatics.scm (gemma)[description]: Use Texinfo
markup.
2021-01-14 20:43:30 +02:00
a36abbe005
gnu: gemma: Update to 0.98.3.
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* gnu/packages/bioinformatics.scm (gemma): Update to 0.98.3.
[source, home-page]: Update to new upstream URI.
[inputs]: Remove eigen, gfortran, lapack.
[arguments]: Remove make-flags. Remove 'find-eigen phase. Rename
'bin-mkdir phase to 'prepare-build and substitute openblas include
directory.
2021-01-14 20:43:30 +02:00
zimoun
610cd6a170
gnu: r-ggbio: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-ggbio): Move from here...
* gnu/packages/bioconductor.scm (r-ggbio): ...to here.
2020-12-29 17:40:28 +01:00
zimoun
81f481d6cd
gnu: r-gqtlstats: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-gqtlstats): Move from here...
* gnu/packages/bioconductor.scm (r-gqtlstats): ...to here.
2020-12-29 17:40:28 +01:00
zimoun
61ec8928c7
gnu: r-snpstats: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-snpstats): Move from here...
* gnu/packages/bioconductor.scm (r-snpstats): ...to here.
2020-12-29 17:40:28 +01:00
zimoun
a2c66d18a5
gnu: r-homo-sapiens: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-homo-sapiens): Move from here...
* gnu/packages/bioconductor.scm (r-homo-sapiens): ...to here.
Replace 'string-append' by 'bioconductor-uri' with 'annotation'.
2020-12-29 17:40:28 +01:00
zimoun
8c2b7c9a2a
gnu: r-erma: Move to (gnu packages bioconductor).
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* gnu/packages/bioinformatics.scm (r-erma): Move from here...
* gnu/packages/bioconductor.scm (r-erma): ...to here.
2020-12-29 17:40:28 +01:00
